An S4 class that information on overlap of target features with annotation features
Get distance to nearest TSS and gene id from AnnotationByGeneParts
Ops method for a ScoreMatrix object. It enables to use arithmetic, indicator and logic operations on ScoreMatrix objects.
Ops method for a ScoreMatrixList object. It enables to use arithmetic, indicator and logic operations on ScoreMatrixList objects.
An S4 class for storing 'getRandomEnrichment' function results
An S4 class for storing 'ScoreMatrix' function results
Get base-pair score for bases in each window
An S4 class for storing a set of 'ScoreMatrixList'
Make ScoreMatrixList from multiple targets
Function to annotate given GRanges object with a given genomic feature
Function to annotate a given GRanges object with promoter,exon,intron & intergenic values
Annotate given ranges with genomic features
Annotate given object with promoter, exon, intron and intergenic regions
Bins the columns of a matrix using a user provided function
Function that computes a maximum value for each bin
Function that computes a mean value for each bin
Function that computes a median value for each bin
Function that computes a minimum value for each bin
Function that computes a sum of values in a bin
function that calculates the significance of overlaps of two sets of features using randomization
convert a data frame read-in from a bed file to a GRanges object for exons
convert a data frame read-in from a bed file to a GRanges object for introns
convert a data frame read-in from a bed file to a GRanges object
Compute an enrichment of IP over control both stored in ScoreMatrix objects
Compute an enrichment of IP (stored in ScoreMatrixList object) over control (stored in ScoreMatrix object)
Compute an enrichment of IP over control both stored in ScoreMatrixList objects
Get the percentage/count of annotation features overlapping with target features from AnnotationByFeature
Function to get upstream and downstream adjecent regions to a genomic feature such as CpG islands
Get the membership slot of AnnotationByFeature
get enrichment based on randomized feature overlap
Get the percentage of target features overlapping with annotation from AnnotationByFeature
Converts a gff formated data.frame into a GenomicRanges object.  The GenomicRanges object needs to be properly formated for the function to work.
Draw a heatmap of a given ScoreMatrix object
Plots the percentage of overlapping intervals with genomic features in a heatmap
Get common rows from all matrices in a ScoreMatrixList object
Function creates a matrix storing data with desirable number of bins for each window
Draw multiple heatmaps from a ScoreMatrixList object
Reorder all elements of a ScoreMatrixList to a given ordering vector
Get scores that correspond to k-mer or PWM matrix occurrence for bases in each window
Plot annotation categories from AnnotationByGeneParts or AnnotationByFeature
function that randomizes the genomic coordinates
Read a BED file and convert it to GRanges.
A function to read the Encode formatted broad peak file into a GRanges object
A function to read-in genomic features and their upstream and downstream adjecent regions such as CpG islands and their shores
Read a tabular file and convert it to GRanges.
A function to read the Encode formatted narrowPeak file into a GRanges object
Function for reading exon intron and promoter structure from a given bed file
Scales the values in the matrix by rows and/or columns
show method for some of the genomation classes
Extract method for a ScoreMatrix object.
Extract method for a ScoreMatrixList object.